Twelve-year-old Gon Freecss one day discovers that the father he had always been told was dead was alive and well. His Father, Ging, is a Hunter—a member of society's elite with a license to go anywhere or do almost anything. Gon, determined to follow in his father's footsteps, decides to take the Hunter Examination and eventually find his father to prove himself as a Hunter in his own right. But on the way, he learns that there is more to becoming a Hunter than previously thought, and the challenges that he must face are considered the toughest in the world.

The story begins with a young boy named Gon, who aspires to be a hunter just like his father Ging. Ging leaves his son in the care of Mito, Gon's aunt, and has not been seen since. Gon catches the local monster fish, "Lord of the Lake", in order to prove his ability to take the exam. Although Mito is reluctant to let Gon leave his home, she relents after he is determined to understand the reason his father left him and his interest of being a hunter.

Gon, Kurapika and Leorio reach Dolle Harbor and are given instructions by the captain to head for the cedar tree on the hilltop behind the city. Moving through a small town, the three are stopped by a group of people, where an old woman gives a question requring them to choose from two choices. Answering wrongly, refusing to answer or attempting to head back will result in failure of the exam.

With the navigators' help, Gon, Kurapika and Leorio arrive at Zaban City, the venue of the exam. The navigator leads them to a small restaurant, which is revealed to be the front for the venue. Gon's group is led to an elevator disguised as a back room, which leads a hundred floors underground. Below, they meet the rest of the participants and given their numbers. There they meet Tonpa, a regular participant who claims to have tried and failed 35 times in the exam.

During the first test, a number of participants fall out from fatigue after running for at least forty kilometers. Leorio almost gives up until he is encouraged by Gon, who waits for him. Killua, a participant, is introduced and he is curious of Gon's personality when he discovers that the boy is the same age as him. Kurapika and Leorio talk about the reason for being a hunter, with Kurapika wanting to take down the Phantom Troupe as his clan was massacred by them for their precious scarlet eyes, which manifest when the Kurta uses their heightened sense. Leorio aims to be a hunter for money, for purely altruistic reasons, as his childhood friend died of an illness without the funds to save him. He wishes to be a doctor so he can give his patients free treatment. Finally, the participants reach the end of the tunnel they are in and up to the surface to the Numere Wetlands, also known as Swindlers' Swamp.

While following Satotz, a fog moves into the swamp and most of the participants are either rendered unconscious or killed by traps and verocious beasts. A group of candidates target Hisoka as they feel he's a threat. Gon and Killua are separated from Leorio and Kurapika and both sides are eventually attacked by monsters. Leorio and Kurapika encounter Hisoka about to be attacked by candidates but are shocked to watch the magician easily take the candidates down. Hisoka then targets Leorio and Kurapika, but realizing that they are no match for him, they decide to head in different directions to stop him from following. However, Leorio returns, unable to run away from a fight. As expected, Leorio is beaten badly by Hisoka. Before the melee can get any worse, Gon, who is separated from Killua, arrives to stop Hisoka. Although he is also no match for Hisoka, he manages to hit his face once before being strangled by Hisoka.

Gon and Kurapika reunite with Leorio and Killua at the Phase Two site. Satotz leads what remains of the candidates to meet the second phase examiners, named Menchi and Buhara. The examiners declare the next phase is to test their cooking skills, much to the candidates' disbelief. The test requires pork, so the candidates are sent to find pigs in the forest. However, the pigs living inside the forest are carnivorous and tear through the candidates. Thanks to Gon, they discover the pigs' weakness and they manage to each get one for their cooking. Upon tasting the candidates' cooking, Buhara gives a pass but Menchi fails all of them. Knowing the candidates will riot, Satotz informs Chairman Netoros of the Hunter Selection Committee to make an appearance. Netoros arrives to correct Menchi's habit of getting biased whenever it's related to cooking. Netoros allows Menchi to stay on as examiner, and she gives the candidates a retest: boil eggs laid by spider eagles on Mt. Split-in-Half.

All the candidates are told by Beans, Neteros' secretary to get their dinner and rest and prepare for the third phase the next morning. Tonpa tries to commit sabotage again by trying to keep Kurapika and Leorio awake for the whole night, but is exasperated to find that none of them fall for his tricks. Gon and Killua explore the airship, and Killua tells Gon that he is actually from a family of assassins. He wished to strike out on his own, which his family has not taken lightly. Neteros arrives and tests both boys' instinct and asks how they felt about the difficulty of the exam. Neteros invites both of them to a game, whoever can grab the ball he is holding before dawn will immediately pass the exam. Gon and Killua find it too hard to pass up, but discovers that with Neteros' skills, they are unable to grab the ball. Eventually Killua realizes that with their skills, they will never be able to take the ball from Neteros for a year, if he keeps it up.

The airship reaches Trick Tower, the Phase Three site, which is a tall featureless pillar built on an equally high platform. The candidates are told that to pass Phase 3, they have to climb down from the top to the base of the tower. An experienced rock climber candidate tries to climb down but is eaten by some flying monsters. Later, Kurapika finds that more than half of the candidates have discovered hidden doors to go inside the tower, which Gon finds one as well. However, the catch is that there are many hidden doors, each one can be only used once and only one person can fit through a door, which means they have to split up. When they try out different doors, they realize that they end up in the same room. In the room, Gon's group are given instructions and special wristwatches for five of them to follow the majority, but they cannot proceed without a fifth member. Lippo, one of the Phase 3 examiners tells them this while explaining they have chosen the path of majority rule.

Tonpa promptly gives up even before Bendot land a punch on him. Leorio is furious at what he has done but Tonpa tells them that his real plan is to sabotage rookies like them. Gon then faces Sedokan, who proposes a match to see whose candle burns the longest. Gon chooses the longer candle, unaware that it is oil-soaked, and his candle starts to burn faster midway. Seeing that his candle is not susceptible to strong winds, he puts it down and sprints towards Sedokan to blow his candle. The next match is between Kurapika and Majitani, who proposes a death match without weapons and and with the condition that one must die or surrender to finish the match. Majitani, who relies on scaring and intimidating his enemies to make them surrender, is easily defeated by Kurapika when he sees something in Majitani and makes him see red.

After winning the bet about Majitani, Leroute, as what the prisoner is named, bets with Leorio about her gender. Despite looking conspicuously female, Leorio, much to Killua and Kurapika's annoyance, bets that she is male. Leorio thinks that team wins if he is correct; and if he is wrong, he will be able to touch Leroute to confirm. Leorio is wrong and goes on to check Leroute. Leorio then challenges Leroute in rock, paper, scissors, and loses. Killua then faces the feared mass murderer Johness the Dissector. Killua rips Johness' heart in an instant and even have it covered in a piece of Johness' cloth. The latter pleads for his heart, and Killua returned it after he is dead. The team thus gathers three points and pass the trial, but they are forced to wait the 50 hours that Leorio has lost with his bets in a small room. Meanwhile, applicants Gittarackur and Hanzo become the second and third one to finish the third phase.

The team stays inside a small room for fifty hours and keep themselves from getting bored. Then they spend the remaining time going to a series of traps and tricks. At the last room, they encountered two doors and are forced to either choose the long and hard path (45 hours) in which all of them may use or the shortcut (about 3 minutes) wherein two of them must be left behind. As disputes break out among them, Gon comes up with an ingenious idea of opening the long way and breaking through the wall to go to the shortcut so all five of them pass this phase.

Gon decides to send a letter to his aunt Mito in order to inform her about the events that had happened during his journey. He started to narrate the story on the events starting from the preliminary Hunter exam to the point when he met Leorio, Kurapika, Killua and the other examinees.

Gon is relying on Bloodcrazy Butterflies to find his target, Hisoka, before waiting for the perfect time to use his skill with the fishing rod to snatch Hisoka's tag. Meanwhile, Leorio is tricked by Tonpa and loses his own tag, but Kurapika helps him recover it. Now that Kurapika and Leorio know that neither is the other's target, they decided to form an alliance.

Kurapika and Leorio are being stalked by Hisoka, but they managed to negotiate their way out of a fight. However, the encounter leaves Hisoka aroused, so he leaves in search of a new target. Gon is able to use his fishing rod to snatch Hisoka's tag right when Hisoka attacks his target. However, as Gon tries to escape, he is attacked by another applicant and loses his tag...

Killua grows tired of having Imori shadowing him so he challenges Imori to a fight and quickly dispatches him. Meanwhile, Gon has joined up with Leorio and Kurapika. The three of them devise a plan for taking Ponzu's tag and track her down to a suspicious-looking cave. That is when Leorio insists on heading in alone.

Gon and his friends have been trapped inside a cave by poisonous snakes. Bourbon, the person responsible for the trap, is already dead, and nobody knows how to disarm the trap. Meanwhile, Leorio, who was bitten by the snakes, is growing weak. Gon manages to get them out of the sticky situation and through to the final phase of the exam. But first, Netero wants an interview with each of the remaining applicants...

Gon and his friends have advanced to the final phase of the Hunter Exam. The final phase is a tournament where the winners are out and the losers advance. The rule is that if you kill your opponent, you'll be disqualified. The first mach is Gon versus Hanzo. Gon can't do anything against Hanzo, but he refuses to give up. Hanzo is losing his patience and threatens to break Gon's arm.

Gon wakes up, and finds himself being congratulated by Satotz for being the first person to pass the Hunter Exam. Gon asks Satotz if the Exam was still going on, and Satotz tells him that it's over. Satotz reveals what happens after he lost consciousness, and Gon finds out some shocking turn of events.

Gon is upset that Killua was forced to kill. Gon is mad at Illumi and proclaims that he will go to Kukuroo Mountain to rescue Killua. As Gon and his friends depart, Satotz mentions that the Hunter Exam isn't over yet...

Gon, Kurapica, and Leorio arrive at Kukuroo Mountain only to find out that they cannot get close to the Zoldyck family estate. The Zoldyck family owns the mountain and all of the surrounding forest and the entire region is gated shut. There is a guard outpost immediately outside of the gate, but instead of serving as a guard, the man working in there actually cleans up the mess created by the watchdog whenever there are intruders into the grounds. Gon, unwilling to give up on "rescuing" Killua, learns from the gatekeeper that the actual door is the massive stone gate and anyone who enters via that path will not be attacked by the watchdog. Leorio tries to pull and push on the gate, to no avail. The gatekeeper informs them that the gate opens up different amounts of stone slabs based only on the strength of the person; however, the least amount of strength anyone needs to open the smallest portion of the door requires two tons of strength on each side.

Gon and his friends have decided to pass through the Trial Gate to see Killua. First, they must train in the servants' residence until they can open the gate. Meanwhile, Killua has learned that Gon and the others are here to see him. Gon, Leorio, and Kurapika are able to open the gate after completing their training, but the apprentice butler Canary stands in their way.

With help from Canary, who is concerned about Killua, Gon and his friends are getting closer to the mansion. However, Kikyo tells them that Killua cannot see them as he is in solitary confinement. Meanwhile, Killua has been summoned by Silva and asked if he wants to see his friend? Killua answers truthfully, and he is allowed to go see his friends...

After reaching the 200th floor, Gon and Killua run into Hisoka's barrier of Nen. They ask Wing to use the violent method for activating their Nen potential. As the deadline for registration draws near, they begin training in one of the four major principles of Nen, Ten.

Gon faces the Nen user Gido in his first 200s Heavens Arena match. Gon uses Ten to protect himself, but he soon finds himself on the defense against Gido's Dancing Tops. As Gon desperately tries to find a way to fight back, he makes a bold decision...

A month has passed since Gon was seriously injured, and Hisoka and Kastro are about to fight in Heavens Arena. Kastro was able to knock Hisoka down in the past and sounds very confident in his interview. Hisoka appears unperturbed by the upcoming fight.

Kastro has used his ability to create a clone of himself with Nen to sever Hisoka's arm and take an advantage in the fight. However, despite losing both arms, Hisoka appears to be perfectly calm. Kastro loses his cool and attacks Hisoka.

After two months, Gon and Killua are finally allowed to practice Nen again. That's when Gido, Sadaso, and Riehlvelt appear before them and tell them to fight them in the arena. Gon and Killua refuse, but Killua finds Sadaso's behavior to be very suspicious.

After landing a punch on Hisoka, Gon returns the tag from the Hunter Exam. Hisoka is ecstatic to see Gon's development and uses his own Nen to attack. Gon is scared, but he recklessly continues to attack! Will he emerge victorious.

After learning Nen and becoming a true Hunter, Gon returns to Whale Island with Killua. When he arrives, Mito has a box for him. She was told by Ging to give this box to Gon once he became a Hunter. However, it appears that the box cannot be opened.

The biggest auction in the world is about to take place in York New City. The Phantom Troupe leader, Chrollo, has instructed the members to gather in the city. For what purpose? The band of murdering thieves is about to make its move.

The auction is finally about to begin. Gon, Killua, and Leorio are working hard to amass enough money to buy Greed Island. Kurapika has been assigned to monitor the auction house. Meanwhile, the Phantom Troupe draws close. All paths will soon cross in York New City.

The Phantom Troupe attacks the underground auction held by the Mafia. Afterwards, there is no sign of the merchandise or guests. The Mafia place a reward on their heads and begin pursuit. Kurapika and the other bodyguards on patrol join the pursuit. Kurapika is drawing closer to the Phantom Troupe.

After Uvogin slaughters the Mafia's pursuit, the Mafia dispatches their secret weapon, the Shadow Beasts. However, Uvogin is able to defeat them by himself. During the battle, the spider tattoo on Uvogin's back is revealed, and Kurapika springs to action.

Kurapika was able to capture Uvogin, a member of the Phantom Troupe. Kurapika struggles to control his rage as Uvogin makes demands as though he isn't a captive. That is when Kurapika receives an e-mail from Hisoka...

Uvogin was able to escape with some help from his fellow bandits. However, after the blow to his pride, he is determined to track down and Kurapika and defeat him. Kurapika realizes that the Phantom Troupe has identified their location and moves the boss to a safe place while awaiting the Phantom Troupe's arrival by himself.

Gon, Killua, and Leorio are trying to get their hands on enough money to buy Greed Island. As they pass through the market, Gon stumbles across a way to identify valuable items. The plan is to buy cheap and sell low, but someone else is bidding on all their items.

Gon and his friends are hoping to win the reward that's been placed on the Phantom Troupe. At the same time, Machi and Nobunaga have been dispatched to search for the "chain user" because Uvogin hasn't returned. Gon and Killua receive a tip and begin shadowing the two Troupe members.

Gon and Killua have been captured by the Phantom Troupe. They are questioned about the chain user that the Troupe is searching for, but the two of them don't know that the chain user is Kurapika. As they're about to be released, Nobunaga decides to keep them around as potential recruits for the Troupe.

The auction has been rescheduled, and the Mafia expects the Phantom Troupe to attack again. The Ten Dons have hired multiple assassins to deal with the Phantom Troupe. Light Nostrade sends Kurapika to join the assassins in dispatching of the Troupe.

The leader of the Phantom Troupe is dead... Kurapika is shocked by the news. Unconvinced, he tries to get a glimpse of the body. Meanwhile, the dead bodies of the other Troupe members have been discovered.

Gon, Killua, Kurapika, and Leorio are finally reunited. Kurapika reveals his Nen powers to the others. However, Killua is afraid that Kurapika is now in danger because one of the Troupe members can read minds. Meanwhile, Chrollo is using the fortune telling power he stole from Neon to tell the fortunes of the Troupe members.

After Chrollo tells fortunes for all of the Troupe members, they suspect that Hisoka has betrayed them. Hisoka's desire to fight Chrollo drives him to take a big risk by altering his own fortune. Meanwhile, after learning that the Troupe is still alive, Kurapika teams up with Gon and friends and work on a plan to capture Pakunoda.

Chrollo uses the information he has on Neon to identify the location of the chain user, Kurapika. Meanwhile, Killua is keeping an eye on the Phantom Troupe base when he is joined by Melody, who helps determine that the Troupe is headed towards Kurapika's hotel. The Troupe is finally closing in on Kurapika.

The Phantom Troupe has learned that Kurapika was the one who killed Uvogin. It's only a matter of time before they realize that the captured Gon and Killua are working with Kurapika? Chrollo takes Gon and killua to the hotel lobby, where Paknoda and the other Troupe members are waiting. Suddenly, the lights go out. Gon and Killua try to escape in the darkness. But Chrollo is the one who has vanished...

The game Greed Island, which holds a clue to finding Ging, is finally on auction. Gon and Killua ask the winning buyer to hire them as players, but they're told that their Nen is too weak. They begin to work on special abilities so they can be selected as players.

Gon and Killua are trying to get themselves chosen as Greed Island players. Tsezgerra, the judge, says that he will make his decision after they show him his Nen. Only 32 of the 200 applicants will pass.

Gon and Killua have finally made it inside the world of Greed Island, their clue to finding Ging. However, all they found was a message from Ging telling Gon to enjoy the game. Their first step is to find a city and gather information. There, they receive an invitation to join a group that's trying to clear the game.

Gon and Killua set off for Masadora in search of spell cards. On the way, they run into many different monsters. However, they struggle against some of the stronger monsters. A girl named Biscuit watches as they fight their way through.